From fb177c4fee051727642a59214787fac4358cb2ed Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 27 Aug 2010 17:35:41 +0000 Subject: [PATCH] If only dcov is specified, assume that selected downsample type is BY_SAMPLE. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4147 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/arguments/GATKArgumentCollection.java | 2 ++ .../sting/gatk/iterators/LocusIteratorByState.java | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 6e1335c3a..efab5c96e 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -143,6 +143,8 @@ public class GATKArgumentCollection { public DownsamplingMethod getDownsamplingMethod() { if(downsamplingType == null && downsampleFraction == null && downsampleCoverage == null) return null; + if(downsamplingType == null && downsampleCoverage != null) + return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE,downsampleCoverage,null); return new DownsamplingMethod(downsamplingType,downsampleCoverage,downsampleFraction); } diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index 4d475b84a..a5902a273 100755 --- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -541,8 +541,8 @@ public class LocusIteratorByState extends LocusIterator { public ReadStateManager(Iterator source, DownsamplingMethod downsamplingMethod, Collection sampleNames) { this.iterator = new PeekableIterator(source); - this.downsamplingMethod = downsamplingMethod; - switch(downsamplingMethod.type) { + this.downsamplingMethod = downsamplingMethod.type != null ? downsamplingMethod : DownsamplingMethod.NONE; + switch(this.downsamplingMethod.type) { case BY_SAMPLE: if(downsamplingMethod.toCoverage == null) throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample");